2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNotNull;
26 import static org.testng.AssertJUnit.assertTrue;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.SequenceFeature;
30 import jalview.gui.AlignFrame;
31 import jalview.schemes.AnnotationColourGradient;
32 import jalview.schemes.GraduatedColor;
34 import java.awt.Color;
36 import java.io.IOException;
39 import org.testng.annotations.Test;
41 public class FeaturesFileTest
44 @Test(groups = { "Functional" })
45 public void testParse() throws Exception
47 File f = new File("examples/uniref50.fa");
48 AlignmentI al = readAlignmentFile(f);
49 AlignFrame af = new AlignFrame(al, 500, 500);
50 Map<String, Object> colours = af.getFeatureRenderer()
52 FeaturesFile featuresFile = new FeaturesFile(
53 "examples/exampleFeatures.txt", FormatAdapter.FILE);
54 assertTrue("Test " + "Features file test"
55 + "\nFailed to parse features file.",
56 featuresFile.parse(al.getDataset(), colours, true));
59 * Refetch the colour map from the FeatureRenderer (to confirm it has been
60 * updated - JAL-1904), and verify (some) feature group colours
62 colours = af.getFeatureRenderer().getFeatureColours();
63 assertEquals("26 feature group colours not found", 26, colours.size());
64 assertEquals(colours.get("Cath"), new Color(0x93b1d1));
65 assertEquals(colours.get("ASX-MOTIF"), new Color(0x6addbb));
68 * verify (some) features on sequences
70 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
71 .getSequenceFeatures(); // FER_CAPAA
72 assertEquals(7, sfs.length);
73 SequenceFeature sf = sfs[0];
74 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
75 assertEquals(39, sf.begin);
76 assertEquals(39, sf.end);
77 assertEquals("uniprot", sf.featureGroup);
78 assertEquals("METAL", sf.type);
80 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
81 assertEquals(44, sf.begin);
82 assertEquals(44, sf.end);
83 assertEquals("uniprot", sf.featureGroup);
84 assertEquals("METAL", sf.type);
86 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
87 assertEquals(47, sf.begin);
88 assertEquals(47, sf.end);
89 assertEquals("uniprot", sf.featureGroup);
90 assertEquals("METAL", sf.type);
92 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
93 assertEquals(77, sf.begin);
94 assertEquals(77, sf.end);
95 assertEquals("uniprot", sf.featureGroup);
96 assertEquals("METAL", sf.type);
98 assertEquals("Fer2 Status: True Positive Pfam 8_8%LINK%",
100 assertEquals("Pfam 8_8|http://pfam.sanger.ac.uk/family/PF00111",
101 sf.links.get(0).toString());
102 assertEquals(8, sf.begin);
103 assertEquals(83, sf.end);
104 assertEquals("uniprot", sf.featureGroup);
105 assertEquals("Pfam", sf.type);
107 assertEquals("Ferredoxin_fold Status: True Positive ", sf.description);
108 assertEquals(3, sf.begin);
109 assertEquals(93, sf.end);
110 assertEquals("uniprot", sf.featureGroup);
111 assertEquals("Cath", sf.type);
114 "High confidence server. Only hits with scores over 0.8 are reported. PHOSPHORYLATION (T) 89_8%LINK%",
117 "PHOSPHORYLATION (T) 89_8|http://www.cbs.dtu.dk/cgi-bin/proview/webface-link?seqid=P83527&service=NetPhos-2.0",
118 sf.links.get(0).toString());
119 assertEquals(89, sf.begin);
120 assertEquals(89, sf.end);
121 assertEquals("netphos", sf.featureGroup);
122 assertEquals("PHOSPHORYLATION (T)", sf.type);
126 * Test parsing a features file with a mix of Jalview and GFF formatted
131 @Test(groups = { "Functional" })
132 public void testParse_mixedJalviewGff() throws Exception
134 File f = new File("examples/uniref50.fa");
135 AlignmentI al = readAlignmentFile(f);
136 AlignFrame af = new AlignFrame(al, 500, 500);
137 Map<String, Object> colours = af.getFeatureRenderer()
138 .getFeatureColours();
139 String gffData = "METAL\tcc9900\n" + "GFF\n"
140 + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n"
141 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
142 FeaturesFile featuresFile = new FeaturesFile(gffData,
143 FormatAdapter.PASTE);
144 assertTrue("Failed to parse features file",
145 featuresFile.parse(al.getDataset(), colours, true));
147 // verify colours read or synthesized
148 colours = af.getFeatureRenderer().getFeatureColours();
149 assertEquals("1 feature group colours not found", 1, colours.size());
150 assertEquals(colours.get("METAL"), new Color(0xcc9900));
152 // verify feature on FER_CAPAA
153 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
154 .getSequenceFeatures();
155 assertEquals(1, sfs.length);
156 SequenceFeature sf = sfs[0];
157 assertEquals("uniprot", sf.description);
158 assertEquals(44, sf.begin);
159 assertEquals(45, sf.end);
160 assertEquals("uniprot", sf.featureGroup);
161 assertEquals("METAL", sf.type);
162 assertEquals(4f, sf.getScore(), 0.001f);
164 // verify feature on FER1_SOLLC
165 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
166 assertEquals(1, sfs.length);
168 assertEquals("uniprot", sf.description);
169 assertEquals(55, sf.begin);
170 assertEquals(130, sf.end);
171 assertEquals("uniprot", sf.featureGroup);
172 assertEquals("Pfam", sf.type);
173 assertEquals(2f, sf.getScore(), 0.001f);
176 public static AlignmentI readAlignmentFile(File f) throws IOException
178 System.out.println("Reading file: " + f);
179 String ff = f.getPath();
180 FormatAdapter rf = new FormatAdapter();
182 AlignmentI al = rf.readFile(ff, FormatAdapter.FILE,
183 new IdentifyFile().identify(ff, FormatAdapter.FILE));
185 al.setDataset(null); // creates dataset sequences
186 assertNotNull("Couldn't read supplied alignment data.", al);
191 * Test various ways of describing a feature colour scheme
195 @Test(groups = { "Functional" })
196 public void testParseGraduatedColourScheme() throws Exception
198 FeaturesFile ff = new FeaturesFile();
201 GraduatedColor gc = ff.parseGraduatedColourScheme(
202 "BETA-TURN-IR\t9a6a94", "label");
203 assertTrue(gc.isColourByLabel());
204 assertEquals(Color.white, gc.getMinColor());
205 assertEquals(Color.black, gc.getMaxColor());
206 assertTrue(gc.isAutoScale());
208 // using colour name, rgb, etc:
209 String spec = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
210 gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
211 assertFalse(gc.isColourByLabel());
212 assertEquals(Color.blue, gc.getMinColor());
213 assertEquals(new Color(255, 0, 255), gc.getMaxColor());
214 assertFalse(gc.isAutoScale());
215 assertFalse(gc.getTolow());
216 assertEquals(20.0f, gc.getMin(), 0.001f);
217 assertEquals(95.0f, gc.getMax(), 0.001f);
218 assertEquals(AnnotationColourGradient.BELOW_THRESHOLD,
220 assertEquals(66.0f, gc.getThresh(), 0.001f);
222 // inverse gradient high to low:
223 spec = "blue|255,0,255|95.0|20.0|below|66.0";
224 gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
225 assertTrue(gc.isAutoScale());
226 assertTrue(gc.getTolow());
230 * Test parsing a features file with GFF formatted content only
234 @Test(groups = { "Functional" })
235 public void testParse_pureGff() throws Exception
237 File f = new File("examples/uniref50.fa");
238 AlignmentI al = readAlignmentFile(f);
239 AlignFrame af = new AlignFrame(al, 500, 500);
240 Map<String, Object> colours = af.getFeatureRenderer()
241 .getFeatureColours();
242 String gffData = "##gff-version 2\n"
243 + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
244 + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
245 + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.";
246 FeaturesFile featuresFile = new FeaturesFile(gffData,
247 FormatAdapter.PASTE);
248 assertTrue("Failed to parse features file",
249 featuresFile.parse(al.getDataset(), colours, true));
251 // verify feature on FER_CAPAA
252 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
253 .getSequenceFeatures();
254 assertEquals(1, sfs.length);
255 SequenceFeature sf = sfs[0];
256 // description parsed from Note attribute
257 assertEquals("Iron-sulfur (2Fe-2S); another note", sf.description);
258 assertEquals(39, sf.begin);
259 assertEquals(39, sf.end);
260 assertEquals("uniprot", sf.featureGroup);
261 assertEquals("METAL", sf.type);
263 "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465",
264 sf.getValue("ATTRIBUTES"));
266 // verify feature on FER1_SOLLC1
267 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
268 assertEquals(1, sfs.length);
270 assertEquals("uniprot", sf.description);
271 assertEquals(55, sf.begin);
272 assertEquals(130, sf.end);
273 assertEquals("uniprot", sf.featureGroup);
274 assertEquals("Pfam", sf.type);
275 assertEquals(3f, sf.getScore(), 0.001f);
279 * Test parsing a features file with Jalview format features (but no colour
280 * descriptors or startgroup to give the hint not to parse as GFF)
284 @Test(groups = { "Functional" })
285 public void testParse_jalviewFeaturesOnly() throws Exception
287 File f = new File("examples/uniref50.fa");
288 AlignmentI al = readAlignmentFile(f);
289 AlignFrame af = new AlignFrame(al, 500, 500);
290 Map<String, Object> colours = af.getFeatureRenderer()
291 .getFeatureColours();
294 * one feature on FER_CAPAA and one on sequence 3 (index 2) FER1_SOLLC
296 String featureData = "Iron-sulfur (2Fe-2S)\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
297 + "Iron-phosphorus (2Fe-P)\tID_NOT_SPECIFIED\t2\t86\t87\tMETALLIC\n";
298 FeaturesFile featuresFile = new FeaturesFile(featureData,
299 FormatAdapter.PASTE);
300 assertTrue("Failed to parse features file",
301 featuresFile.parse(al.getDataset(), colours, true));
303 // verify FER_CAPAA feature
304 SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
305 .getSequenceFeatures();
306 assertEquals(1, sfs.length);
307 SequenceFeature sf = sfs[0];
308 assertEquals("Iron-sulfur (2Fe-2S)", sf.description);
309 assertEquals(39, sf.begin);
310 assertEquals(39, sf.end);
311 assertEquals("METAL", sf.type);
313 // verify FER1_SOLLC feature
314 sfs = al.getSequenceAt(2).getDatasetSequence().getSequenceFeatures();
315 assertEquals(1, sfs.length);
317 assertEquals("Iron-phosphorus (2Fe-P)", sf.description);
318 assertEquals(86, sf.begin);
319 assertEquals(87, sf.end);
320 assertEquals("METALLIC", sf.type);